Figure 4

Analysis of differential crosslinking sites observed in MCF7 versus HEK293 cell lines. (A-C) Browser view of three representative genomic loci encoding differentially occupied transcript regions. Consensus T-C transition profile and read coverage of MCF7 (top) and HEK293 (bottom) are indicated in black and orange, respectively. (A) Dashed red box indicates a position of elevated occupancy in MCF7 versus HEK293 cells in the 3' UTR of the ARID1A transcript. This region coincides with an annotated ELAVL1/HuR binding site previously identified by PAR-CLIP [15]. (B) Region of significantly decreased occupancy in MCF7 versus HEK293 cells in the 3' UTR of CBX3. (C) Genomic loci encoding the long intervening non-coding RNA lincRNA EPHA6-1. Regions with increased protein occupancy in MCF7 cells are apparent (D) Empirical cumulative distribution of the distance to the closest differential T-C transition position (FDR <0.1) for all T-C transitions exhibiting a significant change (red) compared to non-differential positions (black). Differential positions are closer to each other, indicating clustering of differentially occupied sites. (E) Boxplot representing distances between significantly differential positions in MCF7 versus HEK293 cells that change towards the same (gray) or opposing direction (white). Differential positions that share the same orientation are found closer to each other. (F) Fraction of positions with a significant decrease (left) or increase (right) in T-C transitions located in different transcript regions. Elevated positions have a clear tendency to distribute towards the 3' UTR. (G) Density of significantly decreased (top) and increased (bottom) T-C transition positions over relative transcript regions. Decreased T-C transition positions are more frequently observed at the 5' and 3' ends of coding sequences, while up-regulated T-C transition positions do not show a positional tendency.